Biology Review Unit 4

Complete dominance 

One allele masks the effect of another allele

Incomplete Dominance

Heterozygous phenotype is a blend of both alleles

Codominance

Heterozygous genotype expresses both alleles

Multiple alleles

More than 2 alleles exist for a gene

Epistasis

One gene affects the expression of another gene 

Principle of Segregation 

1) Alleles of a gene or gene pairs end up segregating during the formation of gametes. 

2) Individuals have 2 copies of each gene

Particulate Inheritance

1) Hereditary determinations (genes) do not blend and are not modified through use.

2) Genes are discrete, unchanging patterns 

3) Traits are passed down through genes and inheritance is acquired through genetic makeup, not changes developed throughout life. 

Mendel’s Law of Dominance

The dominant allele will mask the effect of the recessive allele in a heterozygous genotype. 

Reciprocal crosses

Reciprocal crosses states that genetic determinants are passed equally from male and female parents. Offspring traits are not dependent on sex of parent contributing the trait.

Mendel’s model states

1) Peas have 2 copies of each gene and may have 2 different alleles.

2) Genes are particles of inheritance and do not blend.

3) Each gamete contains only one copy of each gene.

4) Male and female parents contribute equally to genotype of offspring.

5) Some alleles are dominant to other alleles. 

Independent Assortment

Alleles of different genes do not stay together when they sort. 

Dependent Assortment 

Alleles of different genes do stay together when they sort. 

Testcross

A testcross can be used to confirm the predictions of the principle of independent assortment. 

The Chromosome Theory of Inheritance

1) Genes are on chromosomes and line up independently before being separated. (Meiosis I)

2) Contains key aspects of segregation and independence. 

Linkage

Tendency of alleles of genes to be inherited together. 

genes on the same chromosome are not inherited independently because they are on the same chromosome. 

Sex-linkage

If a gene is on a sex chromosome, then not every gamete will receive on allele of that gene.

Dr. Esther Miriam Zimmer Lederberg (1922-2006) 

American microbiologist, pioneer of bacterial genetics, discovered lambda phage (virus) and fertility factor F, invented replica plating. 

Genetic Code Characteristics

1) Redundant: all but 2 amino acids have > 1 codon. 

2) Unambiguous: one codon = one amino acid (specificity ensures correct assembly of proteins) 

3) Non-overlapping: codons read one at a time (each codon will code for one specific amino acid). 

4) Nearly universal: all codons specify the same amino acids in all organisms. 

5) Conservative: if > 1 codon for an amino acid, first two bases are usually the same. 

Mutations

Any permanent change in DNA

What are the 2 major types of mutations?

1) Point mutation: one or a small number of base changes 

2) Chromosomal-level mutation:  larger at scale

What are the 4 major types of mutations: 

1) Missense Mutation: change in the nucleotide sequence that changes the amino acid specified by a codon/ one amino altered.

2) Silent Mutation: change in the nucleotide sequence that does not change the amino acid specified by a codon (redundant)

3) Nonsense Mutation: change in the nucleotide sequence that results in an early stop codon (ends protein synthesis early)

4) Frameshift Mutation: Addition or deletion of nucleotide from DNA sequence which alters subsequent codons (lead to different sequence of amino acid and proteins) 

Biological fitness

Refers to the ability of an organism to survive and reproduce in its environment 

How is fitness determined?

By seeing how well an organism’s traits respond to the demands of its environment. 

Beneficial mutations

Increase fitness

Neutral mutations

No effect on fitness

Deleterious mutations

Decrease fitness; mutation in an organism’s DNA that is harmful and decreases ability to survive. 

Chromosome-level mutations

1) Can change chromosome number and or structure. 

2) Can be beneficial, neutral, or deleterious.

Types of chromosome-level mutations

1) Deletion: segment of chromosome removed 

2) Inversion: segment of chromosome inverted; genes oriented differently 

3) Duplication: segment of genes duplicated; 2 of each gene on chromosomes 

4) Translocation: segment of one chromosome breaks off and attaches to a different chromosome which results in unusual arrangement of genetic material. 

Dr. Cristiane

1) German Biologist

2) Research on early embryonic development (fruit flies’ model)

3) Discovered the genes responsible for directing cells to form different types with colleagues. 

4) Nobel Prize in Medicine or Physiology in 1995

5) Into microbiology, genetics, and flies 

Transcription

The process of transcribing information/instructions from DNA into mRNA using RNA polymerase. 

What binds to RNA polymerase in both prokaryotes and eukaryotes to start transcription?

Protein

What is the protein used in prokaryotes for transcription?

Sigma (part of RNA polymerase holoenzyme that localizes and binds to the specific promoter region of DNA to start RNA synthesis in the correct site. 

What is the protein used in eukaryotes for transcription?

Eukaryotes use many different proteins but recognizes the starting point which is the promoter for transcription.

What is the promoter? 

The promoter is a region on the DNA sequences where RNA polymerase binds to for transcription to initiate. 

What is translation?

tRNA molecules that end up bringing amino acids to mRNA where they bind through tRNA’s anticodon region and mRNA codon region. mRNA will accept these amino acids and will then build proteins. 

What are the 3 steps that occur in Protein Synthesis?

1) The correct tRNA enters the A site.

2) Peptide bond formation between amino acid on tRNA in A site and P site. 

3) Ribosome moves 1 codon down mRNA and tRNA shifts one position. 

What are all the sites in tRNA and what ends up happening in each site?

1) A site holds incoming aminoacyl tRNA and when ribosome is ready to add another amino acid, the tRNA in the A site pairs with mRNA codon. 

2) P site holds tRNA attached to the growing polypeptide chain. Peptide bond formation occurs and the amino acid from tRNA in the A site is transferred to the polypeptide chain held by tRNA in the P site. 

3) E site is where tRNA exits after it has discharged its amino acid and tRNA released from the ribosome, allowing the ribosome to continue translation process with incoming aminoacyl tRNA.

Dr. William Augustus Hinton (1883-1959)

1) Parents emancipated slaves 

2) Graduated from HMS in 3 years

3) Received 2 merit-based awards, Wiggle worth and the Hayden.  

4) Wrote textbook on syphilis and helped develop the Hinton Flocculation test for it. 

Transcriptional control

most efficient, slowest mechanism (initiation, elongation, termination) talks about mRNA synthesis and stability from DNA

Translational control

faster, many mechanisms (regulates lifespan of mRNA molecules, and sees how often translation begins) 

Post-translational control

Most rapid, least efficient (involves various modifications to proteins which impacts interactions, degradation, and activity) 

Regulon

genes/operons that have the same regulatory sequence (controlled by a single regulatory protein)

Operons

a set of coordinately regulated bacterial genes, transcribed together into one mRNA.

Lac operon

can act as an inducer and impacts whether transcription is able to occur based on interactions with repressor protein; consists of genes responsible for lactose metabolism, illustrating how bacteria adapt to nutrient availability in their environment.

Wobble Hypothesis

The anticodon of tRNA can bind to a codon whose third nucleotide exhibits non-standard base pairing. This allows one tRNA to pair with more than one codon.

Gene regulation: Eukaryotes

• Genes are regulated at multiple levels.

  • Transcriptional control: Prevents gene transcription.

  • Translational control: Prevents mRNA translation.

  • Post-translational control: Disrupts post-translational modification before a protein becomes active

What are the six levels of gene expression in Eukaryotes?

There are six levels of gene expression control in eukaryotes:

1. Chromatin remodeling

2. Transcriptional control

3. RNA processing

4. mRNA stability

5. Translational control

6. Post-translational control

Chromatin Remodeling

• DNA + histone proteins = chromatin.

• RNA polymerase can't access DNA when it is tightly wound.

• Chromatin remodeling unwinds DNA of particular genes so that it can be transcribed.

• Chromatin must be unwound (decondensed) for RNA polymerase to access the promoter.

What are the two types of chromatin?

• "Closed" chromatin: tight DNA-protein interactions.

• "Open" chromatin: some DNA not closely bound to proteins.

What is the chromatin structure?

• Chromatin structure = nucleosomes.

  • A nucleosome is DNA wrapped around histones.

  • A nucleosome contains DNA and linker DNA.

What are the major players in chromosome alteration?

• Major players in chromatin alteration:

  1. DNA methylation

  2. Histone modification

  3. Chromatin-remodeling complexes

DNA Methylation

• Enzymes add methyl groups to cytosine.

• Causes chromatin to condense. (DNA molecules become tightly packed and leads to gene silencing)

Euchromatin

Euchromatin: Regions with high transcriptional activity are loosely packed.

Heterochromatin

Heterochromatin: Regions with low or no transcriptional activity are densely packed.

Epigenetics

The study of how environmental factors influence gene expression without altering the DNA sequence itself. (explains how genes turn off and on, through chemical modifications on DNA)

Enhancers

far from the promoter and generate transcription from a distance by interacting with transcription factors and proteins; provide binding sites for regulatory proteins and recruit RNA polymerase to bind to promoter to start transcription. 

Silencers

far from promoter and repress gene expression by binding to repressor proteins that inhibit transcription. when repressor protein binds to silencers, RNA polymerase is blocked from binding to promoter. 

What are regulatory trancription factors?

RTS are factors that bind to enhancers or silencers to activate or regulate gene expression.

RNA interference (RNAIi)

• controls the lifespan of mRNAs.

• Single-stranded miRNA binds to transcript and destroys or blocks translation.

• A single microRNA can regulate many mRNAs.

• miRNAs regulate the expression of most genes.

• miRNAs are small non-coding regions RNA molecules and bind to target mRNA to either promote degradation of mRNA or inhibit translation. 

Co-regulated genes

Genes in eukaryotes that are activated or repressed together.

Where is DNA packaging in prokaryotes?

In prokaryotic cells, DNA is organized and packed into the cytoplasmic region known as the nucleoid. The DNA is twisted by a process called supercoiling, which involves twisting the DNA more tightly than its normal relaxed state. This supercoiled DNA is held together with proteins that have positive charges, allowing it to fit within the small space of the bacterial cell. The DNA is organized into large loops and is held in place by proteins that prevent it from escaping the nucleoid region

Father (Arthur Kornberg) 

1) Won Nobel Prize in Physiology or Medicine for mechanisms of RNA and DNA synthesis.

2) Mapped process of transcription in yeast and determined the structure of RNAA polymerase (1990s)

3) Proteins are conserved across many eukaryotic organisms

4) Won Nobel Prize in Chemistry (2006) for “work on molecular basis of eukaryotic transcription.”